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Proceedings of the National Academy of Sciences of the United States of America2014; 111(52); 18655-18660; doi: 10.1073/pnas.1412627111

Speciation with gene flow in equids despite extensive chromosomal plasticity.

Abstract: Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.
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Publication Date: 2014-12-01 PubMed ID: 25453089PubMed Central: PMC4284605DOI: 10.1073/pnas.1412627111Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research study focuses on the genetic evolution of equine species – horses, asses, and zebras. Despite significant chromosomal changes, evidence of gene flow and speciation was found among all of these species, providing insights on how chromosomal structure influences gene flow and speciation.

Research Objective and Methodology

  • The research aims to understand the genetic evolution and speciation among equine species, including horses, asses, and zebras, despite their chromosomal differences. The genus Equus emerged around 4.0 to 4.5 million years ago (Mya), and the succession of events leading to the diversity of species today remains unclear.
  • For the analysis, the researchers sequenced six genomes from each extant species of asses and zebras. The genome of an extinct quagga zebra was also characterized using a museum specimen.

Key Findings

  • The researchers identified 48 genes that evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. This suggests that these genes might play a key role in the specific adaptations of the equine species.
  • The study presents a dynamic demographic history of equids, with synchronous expansions and collapses on different continents during the last 400,000 years, majorly influenced by climatic events.
  • The earliest speciation was found to have occurred in Northern America, with the ancestors of today’s asses and zebras dispersing into the Old World (Eurasia and Africa) 2.1 to 3.4 Mya.
  • Despite the difference in chromosomal count varying from 16 pairs to 31 pairs, evidence for gene flow amongst three contemporary equine species was found. This challenges the belief that accumulation of chromosomal rearrangements leads to complete reproductive isolation.

Implications of the Study

  • The findings promote equids as a primary model for understanding the relationship between chromosomal structure, gene flow, and speciation.
  • This study could impact future research on genetic evolution and offer a greater understanding of how species diversify over time.
  • It also provides a genomic basis for past demographic events impacting equine species, opening avenues for studying the impact of climatic and environmental changes on genetic diversification.

Cite This Article

APA
Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. (2014). Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc Natl Acad Sci U S A, 111(52), 18655-18660. https://doi.org/10.1073/pnas.1412627111

Publication

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
NlmUniqueID: 7505876
Country: United States
Language: English
Volume: 111
Issue: 52
Pages: 18655-18660

Researcher Affiliations

Jónsson, Hákon
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Schubert, Mikkel
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Seguin-Orlando, Andaine
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark; National High-Throughput DNA Sequencing Center, DK-1353 Copenhagen K, Denmark;
Ginolhac, Aurélien
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Petersen, Lillian
  • National High-Throughput DNA Sequencing Center, DK-1353 Copenhagen K, Denmark;
Fumagalli, Matteo
  • Department of Integrative Biology, University of California, Berkeley, CA 94720; UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom;
Albrechtsen, Anders
  • The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark;
Petersen, Bent
  • Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark;
Korneliussen, Thorfinn S
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Vilstrup, Julia T
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Lear, Teri
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Myka, Jennifer Leigh
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Lundquist, Judith
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Miller, Donald C
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853;
Alfarhan, Ahmed H
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Alquraishi, Saleh A
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Al-Rasheid, Khaled A S
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Stagegaard, Julia
  • Ree Park, Ebeltoft Safari, DK-8400 Ebeltoft, Denmark;
Strauss, Günter
  • Tierpark Berlin-Friedrichsfelde, 10319 Berlin, Germany; and.
Bertelsen, Mads Frost
  • Centre for Zoo and Wild Animal Health, Copenhagen Zoo, DK-2000 Frederiksberg, Denmark.
Sicheritz-Ponten, Thomas
  • Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark;
Antczak, Douglas F
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853;
Bailey, Ernest
  • Maxwell H. Gluck Equine Research Center, Veterinary Science Department, University of Kentucky, Lexington, KY 40546;
Nielsen, Rasmus
  • Department of Integrative Biology, University of California, Berkeley, CA 94720;
Willerslev, Eske
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark;
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark; Lorlando@snm.ku.dk.

MeSH Terms

  • Africa
  • Animals
  • Chromosomes, Mammalian / genetics
  • Equidae / genetics
  • Evolution, Molecular
  • Extinction, Biological
  • Gene Flow
  • North America

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

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